Gov. Andrew M. Cuomo is a skilled back-room operator, renowned for pressuring allies and foes behind the scenes to achieve results that show him in the best possible light.

But in Preet Bharara, the United States attorney for the Southern District of New York, he has encountered an adversary who seems eager for the spotlight and is challenging the very way the governor does business.

Mr. Bharara, who made his reputation prosecuting insider traders and corrupt legislators, first surfaced as a problem for Mr. Cuomo in April, when his outrage spilled into public view and he began an investigation after the governor abruptly shut down a commission he had set up to clean up corruption in Albany.

The commission had been looking at improper campaign spending by lawmakers, among other things. Mr. Bharara took over the cases it was working on, but also began investigating whether the governor’s office interfered with investigations and the circumstances surrounding the panel’s shutdown.

What followed has included reports of grand jury subpoenas, a parade of members of the commission and its staff to Mr. Bharara’s office to be interviewed about the panel’s work and its shutdown, suggestions that the governor’s office has not moved fast enough in having subpoenaed documents turned over by the commission and the hiring of criminal defense lawyers by witnesses and potential targets, the governor’s office itself included.

But Mr. Bharara’s investigation into the disbanding of the panel, known as the Moreland Commission, took on a new and more volatile dimension on Wednesday, when his office warned that attempts by Mr. Cuomo or his allies to line up public statements supporting the governor from members of the defunct commission — the sort of coordinated political response for which Mr. Cuomo, a Democrat, is well known — could constitute criminal witness tampering or obstruction of justice.

The very public collision between Mr. Cuomo and Mr. Bharara, which comes a little over three months before the governor seeks re-election, is unlike any that Mr. Cuomo has faced in his political career.

As state attorney general, he led an investigation into then-Gov. Eliot Spitzer, damaging Mr. Spitzer’s reputation in advance of his later undoing in a prostitution scandal. Mr. Cuomo’s disdain for his fellow Democrats Eric T. Schneiderman, the attorney general, and Thomas P. DiNapoli, the comptroller, has been widely documented, but neither has publicly taken him on. This year, he outmaneuvered another Democrat, Mayor Bill de Blasio, over taxes and charter schools, but inflicted only glancing blows, and Mr. de Blasio this week felt compelled to defend Mr. Cuomo as “a person of high integrity” and “an agent of reform.”

No countermove in Mr. Cuomo’s extensive political playbook seemed to apply to his latest rival, Mr. Bharara: a federal prosecutor free of the co-dependencies that often lead Albany lawmakers to shy away from conflict with the state’s most powerful politician.

“Andrew’s M.O. — behind-the-curtain string-pulling — yesterday crashed into an immovable object called Preet Bharara,” said Mark Green, a former New York City public advocate who unsuccessfully ran against Mr. Cuomo for the attorney general’s office in 2006. “He now has to alter his penchant for off-the-record carrots and sticks,” Mr. Green added, “because there’s no off-the-record when anyone can be subpoenaed, including him.”

Mr. Bharara, who grew up in New Jersey, learned politics from two masters. As a young man he was an intern for Mr. Cuomo’s father, former Gov. Mario M. Cuomo. And he later served as chief counsel for Senator Charles E. Schumer, whose relationship with Andrew Cuomo is not close.

Mr. Bharara, who was nominated for his post by President Obama in 2009, has said he has no political aspirations, an assertion that is believed by some but not others. But he is showing no sign of letting up on his scrutiny of Mr. Cuomo and his aides.

In an interview last week with Charlie Rose, Mr. Bharara said his office had “the kind of fearlessness and independence that is required to do difficult public corruption cases.”

The confrontation between Mr. Bharara and Governor Cuomo intensified over the course of a week that began with the July 23 publication in The New York Times of a three-month examination of the Moreland Commission’s short life span, which found that the governor and his aides had hobbled the panel’s work, intervening repeatedly when it focused on groups with ties to Mr. Cuomo or issues that could reflect negatively on him.

Mr. Cuomo disappeared from view amid a hailstorm of criticism, then, on Monday, emerged with a defiant retort: As if on cue, several members of the commission issued statements defending him. Crucially, one of the panel’s co-chairmen, William J. Fitzpatrick, asserted that “nobody ‘interfered’ with me or my co-chairs.” Calling Mr. Fitzpatrick authoritative, Mr. Cuomo said that he had done nothing wrong and that the panel’s independence had never been compromised.

(The endorsing statements by commissioners were a familiar Cuomo move: Earlier this year, when the governor was locked in a battle with Mr. de Blasio over prekindergarten, reporters at one point were suddenly pelted with unsolicited statements from mayors and county executives who sided with Mr. Cuomo.)

By Wednesday morning, the storm almost seemed over. Mr. Cuomo appeared on Long Island, wielding the instruments of his power to issue relief to victims of Hurricane Sandy, and easily dispensing with the few questions he faced about the Moreland Commission.

But late that afternoon, Mr. Bharara’s office sent a letter to a lawyer for the commission, citing the continuing federal investigation, alluding to the statements on Monday by commissioners supportive of Mr. Cuomo and warning that attempts to influence or tamper with the recollections of any witnesses could violate federal law.

The statements defending Mr. Cuomo appeared to catalyze a growing sense of frustration in the office of Mr. Bharara.

His investigators had already questioned delays in receiving thousands of emails and other documents they had subpoenaed from the panel more than two months ago, people briefed on the matter said. The reason for the delay: Mr. Cuomo’s budget office only days ago approved a contract with the lawyer retained to represent the anticorruption panel. The lawyer, Michael L. Koenig, has as a result been unable to pay a company to process and sort the documents, which were already handed over to him by commission members and employees.

The statements on Monday, and the possibility that they were elicited at the governor’s behest, only inflamed prosecutors: Commissioners, after all, were potential witnesses in the investigation into Mr. Cuomo’s office.

And there was already a view among investigators that Mr. Fitzpatrick, the co-chairman whose statement Mr. Cuomo called definitive, had changed his story, people briefed on the matter said. Mr. Fitzpatrick, the Onondaga County district attorney, did not respond on Thursday to a request for comment.

During the commission’s tenure, as The Times reported, Mr. Fitzpatrick privately expressed frustration about meddling, emailing colleagues at one point that the governor’s office needed “to understand this is an INDEPENDENT commission and needs to be treated as such,” and adding, “Does the governor really want mass resignations?!”

And on April 9, in a meeting with Mr. Bharara and other federal investigators, Mr. Fitzpatrick voiced his frustrations with meddling by the governor’s office in the panel’s investigations, according to a person familiar with the meeting who insisted on anonymity for fear of reprisal.

On Thursday, Mr. Cuomo issued a new statement, saying the statements on Monday had been solicited only “to correct the public record.”

As Mr. Bharara “has made it clear that ongoing public dialogue is not helpful to his investigation,” Mr. Cuomo added, “we will have no additional comment on the matter.”

A version of this article appears in print on , on Page A1 of the New York edition with the headline: Cuomo’s Back-Room Style Draws a Potent Critic. Order Reprints | Today’s Paper | Subscribe